Brickskeller in DC just because of their amazing selection
Mentioned a lot in this thread, and they are very good, but they're not even in the running for best in the country. Their list is huge but they're often out of the first 3-4 things I order, and service tends toward the slow side. They've finally expanded from a meager 2 taps to 12, but the selection's never been as interesting as at RFD or elsewhere in the area.
I can think of 4 places just in the DC area where I'd rather go for a beer:
Rustico, Alexandria: 50 beers on tap, 5 cask-conditioned ales, 500+ bottles, they have a beer steward to do beer pairings with your meal, and good food. Noisier atmosphere during peak hours is the main drawback.
RFD Drafthouse, DC: Same owners as Brickskeller, 30 taps and one cask-conditioned pump. At most one BMC among the taps, so a great selection of fresh draught beer.
Bilbo Baggins, Alexandria: 10 taps, all with interesting stuff (no BMC at all), plus a decent selection of bottles (20+ Belgians, for instance, maybe 50-70 in total but a pretty neat selection) and I've not had anything out of stock when ordering. Plus 180+ wines if you have mixed company.
For bottles only:
Lost Dog Cafe, Arlington: Great sandwiches. There's a 3 beer limit per customer--but all of their (400+) beers are available to go in 6 packs (or however they're packaged). A great place to have dinner, try 3 things you've never had, and pick up whatever you like.
But back to the main question, IMO the best beer bar in the country is the
Great Lost Bear in Portland, ME. 60+ taps, 4 cask-conditioned pumps (including Allagash Confluence currently!), great food, and great atmosphere. There's a focus on local stuff and Belgians, but with that many taps there's plenty of room for Dogfish 90, Rogue Yellow Snow, Stone Double Bastard, Brooklyn Savoir Faire, etc.